Hi Amirhossein

it's hard to tell without looking at the data, but you could try using the expert options to change the allowable intensity ranges for the different surfaces (e.g. if the white is too far out, don't allow mris_make_surfaces to put the gray/white border at intensities that are that dark)

cheers
Bruce

On Mon, 17 Feb 2014, amirhossein manzouri wrote:

Hi all, 
There is incorrect pial surface lines (red and yellow) in the right
hemisphere of some of my subjects. The white matter and grey matter are very
close regarding intensity and this can be seen in just a few slices and then
it gets correct. I tried control points but regarding the low intensity they
can be effective. I wonder if there is a way to correct this, or if they may
affect the qdec analysis between group afterwards a lot.(since they are
present in one or few slices and create thick GM in those slices!)

Best regards,
Amirhossein Manzouri 

 

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